X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FJalviewChimeraBinding.java;h=399bad9d9c9d7cd0982644529885594e7bedea43;hb=b7cd96eaeb85474ee2ddec1de92181a3b88ceece;hp=2171815ac77c99dede609be1a9d755a81bb666ed;hpb=f831ddf7f52d6c4a1918e87d94877b22bd322648;p=jalview.git diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java index 2171815..399bad9 100644 --- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java +++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java @@ -20,29 +20,13 @@ */ package jalview.ext.rbvi.chimera; -import jalview.api.AlignmentViewPanel; -import jalview.api.FeatureRenderer; -import jalview.api.SequenceRenderer; -import jalview.api.structures.JalviewStructureDisplayI; -import jalview.bin.Cache; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.ColumnSelection; -import jalview.datamodel.PDBEntry; -import jalview.datamodel.SequenceI; -import jalview.httpserver.AbstractRequestHandler; -import jalview.io.DataSourceType; -import jalview.schemes.ColourSchemeI; -import jalview.schemes.ResidueProperties; -import jalview.structure.AtomSpec; -import jalview.structure.StructureMappingcommandSet; -import jalview.structure.StructureSelectionManager; -import jalview.structures.models.AAStructureBindingModel; -import jalview.util.MessageManager; - -import java.awt.Color; +import java.io.File; +import java.io.FileOutputStream; +import java.io.IOException; +import java.io.PrintWriter; import java.net.BindException; import java.util.ArrayList; -import java.util.Hashtable; +import java.util.Collections; import java.util.LinkedHashMap; import java.util.List; import java.util.Map; @@ -51,29 +35,33 @@ import ext.edu.ucsf.rbvi.strucviz2.ChimeraManager; import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel; import ext.edu.ucsf.rbvi.strucviz2.StructureManager; import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType; +import jalview.api.AlignmentViewPanel; +import jalview.bin.Console; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SearchResultMatchI; +import jalview.datamodel.SearchResultsI; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceI; +import jalview.gui.StructureViewer.ViewerType; +import jalview.httpserver.AbstractRequestHandler; +import jalview.io.DataSourceType; +import jalview.structure.AtomSpec; +import jalview.structure.AtomSpecModel; +import jalview.structure.StructureCommand; +import jalview.structure.StructureCommandI; +import jalview.structure.StructureSelectionManager; +import jalview.structures.models.AAStructureBindingModel; public abstract class JalviewChimeraBinding extends AAStructureBindingModel { - // Chimera clause to exclude alternate locations in atom selection - private static final String NO_ALTLOCS = "&~@.B-Z&~@.2-9"; - - private static final String COLOURING_CHIMERA = MessageManager - .getString("status.colouring_chimera"); - - private static final boolean debug = false; + public static final String CHIMERA_SESSION_EXTENSION = ".py"; - private static final String PHOSPHORUS = "P"; + public static final String CHIMERA_FEATURE_GROUP = "Chimera"; - private static final String ALPHACARBON = "CA"; - - private List chainNames = new ArrayList(); - - private Hashtable chainFile = new Hashtable(); - /* * Object through which we talk to Chimera */ - private ChimeraManager viewer; + private ChimeraManager chimeraManager; /* * Object which listens to Chimera notifications @@ -81,47 +69,27 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel private AbstractRequestHandler chimeraListener; /* - * set if chimera state is being restored from some source - instructs binding - * not to apply default display style when structure set is updated for first - * time. - */ - private boolean loadingFromArchive = false; - - /* - * flag to indicate if the Chimera viewer should ignore sequence colouring - * events from the structure manager because the GUI is still setting up - */ - private boolean loadingFinished = true; - - /* * Map of ChimeraModel objects keyed by PDB full local file name */ - private Map> chimeraMaps = new LinkedHashMap>(); - - /* - * the default or current model displayed if the model cannot be identified - * from the selection message - */ - private int frameNo = 0; - - private String lastCommand; + protected Map> chimeraMaps = new LinkedHashMap<>(); String lastHighlightCommand; - /* - * incremented every time a load notification is successfully handled - - * lightweight mechanism for other threads to detect when they can start - * referring to new structures. + /** + * Returns a model of the structure positions described by the Chimera format atomspec + * @param atomSpec + * @return */ - private long loadNotifiesHandled = 0; - - private Thread chimeraMonitor; + protected AtomSpec parseAtomSpec(String atomSpec) + { + return AtomSpec.fromChimeraAtomspec(atomSpec); + } /** * Open a PDB structure file in Chimera and set up mappings from Jalview. * - * We check if the PDB model id is already loaded in Chimera, if so don't - * reopen it. This is the case if Chimera has opened a saved session file. + * We check if the PDB model id is already loaded in Chimera, if so don't reopen + * it. This is the case if Chimera has opened a saved session file. * * @param pe * @return @@ -131,8 +99,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel String file = pe.getFile(); try { - List modelsToMap = new ArrayList(); - List oldList = viewer.getModelList(); + List modelsToMap = new ArrayList<>(); + List oldList = chimeraManager.getModelList(); boolean alreadyOpen = false; /* @@ -153,16 +121,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel */ if (!alreadyOpen) { - viewer.openModel(file, pe.getId(), ModelType.PDB_MODEL); - List newList = viewer.getModelList(); - // JAL-1728 newList.removeAll(oldList) does not work - for (ChimeraModel cm : newList) - { - if (cm.getModelName().equals(pe.getId())) - { - modelsToMap.add(cm); - } - } + chimeraManager.openModel(file, pe.getId(), ModelType.PDB_MODEL); + addChimeraModel(pe, modelsToMap); } chimeraMaps.put(file, modelsToMap); @@ -170,13 +130,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel if (getSsm() != null) { getSsm().addStructureViewerListener(this); - // ssm.addSelectionListener(this); - FeatureRenderer fr = getFeatureRenderer(null); - if (fr != null) - { - fr.featuresAdded(); - } - refreshGUI(); } return true; } catch (Exception q) @@ -189,6 +142,31 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } /** + * Adds the ChimeraModel corresponding to the given PDBEntry, based on model + * name matching PDB id + * + * @param pe + * @param modelsToMap + */ + protected void addChimeraModel(PDBEntry pe, + List modelsToMap) + { + /* + * Chimera: query for actual models and find the one with + * matching model name - already set in viewer.openModel() + */ + List newList = chimeraManager.getModelList(); + // JAL-1728 newList.removeAll(oldList) does not work + for (ChimeraModel cm : newList) + { + if (cm.getModelName().equals(pe.getId())) + { + modelsToMap.add(cm); + } + } + } + + /** * Constructor * * @param ssm @@ -197,368 +175,64 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * @param protocol */ public JalviewChimeraBinding(StructureSelectionManager ssm, - PDBEntry[] pdbentry, SequenceI[][] sequenceIs, DataSourceType protocol) + PDBEntry[] pdbentry, SequenceI[][] sequenceIs, + DataSourceType protocol) { super(ssm, pdbentry, sequenceIs, protocol); - viewer = new ChimeraManager(new StructureManager(true)); + boolean chimeraX = ViewerType.CHIMERAX.equals(getViewerType()); + chimeraManager = chimeraX ? new ChimeraXManager(new StructureManager(true)) : new ChimeraManager(new StructureManager(true)); + setStructureCommands(chimeraX ? new ChimeraXCommands() : new ChimeraCommands()); } - /** - * Starts a thread that waits for the Chimera process to finish, so that we - * can then close the associated resources. This avoids leaving orphaned - * Chimera viewer panels in Jalview if the user closes Chimera. - */ - protected void startChimeraProcessMonitor() + @Override + protected ViewerType getViewerType() { - final Process p = viewer.getChimeraProcess(); - chimeraMonitor = new Thread(new Runnable() - { - - @Override - public void run() - { - try - { - p.waitFor(); - JalviewStructureDisplayI display = getViewer(); - if (display != null) - { - display.closeViewer(false); - } - } catch (InterruptedException e) - { - // exit thread if Chimera Viewer is closed in Jalview - } - } - }); - chimeraMonitor.start(); + return ViewerType.CHIMERA; } /** - * Start a dedicated HttpServer to listen for Chimera notifications, and tell - * it to start listening + * Start a dedicated HttpServer to listen for Chimera notifications, and tell it + * to start listening */ public void startChimeraListener() { try { chimeraListener = new ChimeraListener(this); - viewer.startListening(chimeraListener.getUri()); + startListening(chimeraListener.getUri()); } catch (BindException e) { - System.err.println("Failed to start Chimera listener: " - + e.getMessage()); - } - } - - /** - * Tells Chimera to display only the specified chains - * - * @param toshow - */ - public void showChains(List toshow) - { - /* - * Construct a chimera command like - * - * ~display #*;~ribbon #*;ribbon :.A,:.B - */ - StringBuilder cmd = new StringBuilder(64); - boolean first = true; - for (String chain : toshow) - { - int modelNumber = getModelNoForChain(chain); - String showChainCmd = modelNumber == -1 ? "" : modelNumber + ":." - + chain.split(":")[1]; - if (!first) - { - cmd.append(","); - } - cmd.append(showChainCmd); - first = false; + System.err.println( + "Failed to start Chimera listener: " + e.getMessage()); } - - /* - * could append ";focus" to this command to resize the display to fill the - * window, but it looks more helpful not to (easier to relate chains to the - * whole) - */ - final String command = "~display #*; ~ribbon #*; ribbon :" - + cmd.toString(); - sendChimeraCommand(command, false); } /** * Close down the Jalview viewer and listener, and (optionally) the associated * Chimera window. */ + @Override public void closeViewer(boolean closeChimera) { - getSsm().removeStructureViewerListener(this, this.getPdbFile()); - if (closeChimera) - { - viewer.exitChimera(); - } + super.closeViewer(closeChimera); if (this.chimeraListener != null) { chimeraListener.shutdown(); chimeraListener = null; } - lastCommand = null; - viewer = null; - - if (chimeraMonitor != null) - { - chimeraMonitor.interrupt(); - } - releaseUIResources(); - } - - @Override - public void colourByChain() - { - colourBySequence = false; - sendAsynchronousCommand("rainbow chain", COLOURING_CHIMERA); - } - - /** - * Constructs and sends a Chimera command to colour by charge - *
    - *
  • Aspartic acid and Glutamic acid (negative charge) red
    • - *
  • Lysine and Arginine (positive charge) blue
    • - *
  • Cysteine - yellow
    • - *
  • all others - white
    • - *
- */ - @Override - public void colourByCharge() - { - colourBySequence = false; - String command = "color white;color red ::ASP;color red ::GLU;color blue ::LYS;color blue ::ARG;color yellow ::CYS"; - sendAsynchronousCommand(command, COLOURING_CHIMERA); - } - - /** - * Construct and send a command to align structures against a reference - * structure, based on one or more sequence alignments - * - * @param _alignment - * an array of alignments to process - * @param _refStructure - * an array of corresponding reference structures (index into pdb - * file array); if a negative value is passed, the first PDB file - * mapped to an alignment sequence is used as the reference for - * superposition - * @param _hiddenCols - * an array of corresponding hidden columns for each alignment - */ - @Override - public void superposeStructures(AlignmentI[] _alignment, - int[] _refStructure, ColumnSelection[] _hiddenCols) - { - StringBuilder allComs = new StringBuilder(128); - String[] files = getPdbFile(); - - if (!waitForFileLoad(files)) - { - return; - } - - refreshPdbEntries(); - StringBuilder selectioncom = new StringBuilder(256); - for (int a = 0; a < _alignment.length; a++) - { - int refStructure = _refStructure[a]; - AlignmentI alignment = _alignment[a]; - ColumnSelection hiddenCols = _hiddenCols[a]; - - if (refStructure >= files.length) - { - System.err.println("Ignoring invalid reference structure value " - + refStructure); - refStructure = -1; - } - - /* - * 'matched' array will hold 'true' for visible alignment columns where - * all sequences have a residue with a mapping to the PDB structure - */ - boolean matched[] = new boolean[alignment.getWidth()]; - for (int m = 0; m < matched.length; m++) - { - matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true; - } - - SuperposeData[] structures = new SuperposeData[files.length]; - for (int f = 0; f < files.length; f++) - { - structures[f] = new SuperposeData(alignment.getWidth()); - } - - /* - * Calculate the superposable alignment columns ('matched'), and the - * corresponding structure residue positions (structures.pdbResNo) - */ - int candidateRefStructure = findSuperposableResidues(alignment, - matched, structures); - if (refStructure < 0) - { - /* - * If no reference structure was specified, pick the first one that has - * a mapping in the alignment - */ - refStructure = candidateRefStructure; - } - - int nmatched = 0; - for (boolean b : matched) - { - if (b) - { - nmatched++; - } - } - if (nmatched < 4) - { - // TODO: bail out here because superposition illdefined? - } - - /* - * Generate select statements to select regions to superimpose structures - */ - String[] selcom = new String[files.length]; - for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) - { - String chainCd = "." + structures[pdbfnum].chain; - int lpos = -1; - boolean run = false; - StringBuilder molsel = new StringBuilder(); - for (int r = 0; r < matched.length; r++) - { - if (matched[r]) - { - int pdbResNum = structures[pdbfnum].pdbResNo[r]; - if (lpos != pdbResNum - 1) - { - /* - * discontiguous - append last residue now - */ - if (lpos != -1) - { - molsel.append(String.valueOf(lpos)); - molsel.append(chainCd); - molsel.append(","); - } - run = false; - } - else - { - /* - * extending a contiguous run - */ - if (!run) - { - /* - * start the range selection - */ - molsel.append(String.valueOf(lpos)); - molsel.append("-"); - } - run = true; - } - lpos = pdbResNum; - } - } - - /* - * and terminate final selection - */ - if (lpos != -1) - { - molsel.append(String.valueOf(lpos)); - molsel.append(chainCd); - } - if (molsel.length() > 1) - { - selcom[pdbfnum] = molsel.toString(); - selectioncom.append("#").append(String.valueOf(pdbfnum)) - .append(":"); - selectioncom.append(selcom[pdbfnum]); - selectioncom.append(" "); - if (pdbfnum < files.length - 1) - { - selectioncom.append("| "); - } - } - else - { - selcom[pdbfnum] = null; - } - } - - StringBuilder command = new StringBuilder(256); - for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) - { - if (pdbfnum == refStructure || selcom[pdbfnum] == null - || selcom[refStructure] == null) - { - continue; - } - if (command.length() > 0) - { - command.append(";"); - } - - /* - * Form Chimera match command, from the 'new' structure to the - * 'reference' structure e.g. (50 residues, chain B/A, alphacarbons): - * - * match #1:1-30.B,81-100.B@CA #0:21-40.A,61-90.A@CA - * - * @see - * https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html - */ - command.append("match ").append(getModelSpec(pdbfnum)).append(":"); - command.append(selcom[pdbfnum]); - command.append("@").append( - structures[pdbfnum].isRna ? PHOSPHORUS : ALPHACARBON); - // JAL-1757 exclude alternate CA locations - command.append(NO_ALTLOCS); - command.append(" ").append(getModelSpec(refStructure)).append(":"); - command.append(selcom[refStructure]); - command.append("@").append( - structures[refStructure].isRna ? PHOSPHORUS : ALPHACARBON); - command.append(NO_ALTLOCS); - } - if (selectioncom.length() > 0) - { - if (debug) - { - System.out.println("Select regions:\n" + selectioncom.toString()); - System.out.println("Superimpose command(s):\n" - + command.toString()); - } - allComs.append("~display all; chain @CA|P; ribbon ") - .append(selectioncom.toString()) - .append(";" + command.toString()); - } - } - if (selectioncom.length() > 0) + + /* + * the following call is added to avoid a stack trace error in Chimera + * after "stop really" is sent; Chimera > 1.14 will not need it; see also + * http://plato.cgl.ucsf.edu/trac/chimera/ticket/17597 + */ + if (closeChimera && (getViewerType() == ViewerType.CHIMERA)) { - // TODO: visually distinguish regions that were superposed - if (selectioncom.substring(selectioncom.length() - 1).equals("|")) - { - selectioncom.setLength(selectioncom.length() - 1); - } - if (debug) - { - System.out.println("Select regions:\n" + selectioncom.toString()); - } - allComs.append("; ~display all; chain @CA|P; ribbon ") - .append(selectioncom.toString()).append("; focus"); - sendChimeraCommand(allComs.toString(), false); + chimeraManager.getChimeraProcess().destroy(); } + chimeraManager.clearOnChimeraExit(); + chimeraManager = null; } /** @@ -578,7 +252,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel { if (pdbfnum < 0 || pdbfnum >= getPdbCount()) { - return ""; + return "#" + pdbfnum; // temp hack for ChimeraX } /* @@ -587,7 +261,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * to the Chimera command 'list models type molecule', see * ChimeraManager.getModelList(). */ - List maps = chimeraMaps.get(getPdbFile()[pdbfnum]); + List maps = chimeraMaps.get(getStructureFiles()[pdbfnum]); boolean hasSubModels = maps != null && maps.size() > 1; return "#" + String.valueOf(pdbfnum) + (hasSubModels ? ".1" : ""); } @@ -601,16 +275,15 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel */ public boolean launchChimera() { - if (viewer.isChimeraLaunched()) + if (chimeraManager.isChimeraLaunched()) { return true; } - boolean launched = viewer.launchChimera(StructureManager - .getChimeraPaths()); + boolean launched = chimeraManager.launchChimera(getChimeraPaths()); if (launched) { - startChimeraProcessMonitor(); + startExternalViewerMonitor(chimeraManager.getChimeraProcess()); } else { @@ -620,146 +293,81 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } /** - * Answers true if the Chimera process is still running, false if ended or not - * started. + * Returns a list of candidate paths to the Chimera program executable * * @return */ - public boolean isChimeraRunning() + protected List getChimeraPaths() { - return viewer.isChimeraLaunched(); + return StructureManager.getChimeraPaths(false); } /** - * Send a command to Chimera, and optionally log any responses. + * Answers true if the Chimera process is still running, false if ended or not + * started. * - * @param command - * @param logResponse + * @return */ - public void sendChimeraCommand(final String command, boolean logResponse) + @Override + public boolean isViewerRunning() { - if (viewer == null) - { - // ? thread running after viewer shut down - return; - } - viewerCommandHistory(false); - if (lastCommand == null || !lastCommand.equals(command)) - { - // trim command or it may never find a match in the replyLog!! - List lastReply = viewer.sendChimeraCommand(command.trim(), - logResponse); - if (logResponse && debug) - { - log("Response from command ('" + command + "') was:\n" + lastReply); - } - } - viewerCommandHistory(true); - lastCommand = command; + return chimeraManager!=null && chimeraManager.isChimeraLaunched(); } /** - * Send a Chimera command asynchronously in a new thread. If the progress - * message is not null, display this message while the command is executing. + * Send a command to Chimera, and optionally log and return any responses. * * @param command - * @param progressMsg - */ - protected abstract void sendAsynchronousCommand(String command, - String progressMsg); - - /** - * Sends a set of colour commands to the structure viewer - * - * @param colourBySequenceCommands + * @param getResponse */ @Override - protected void colourBySequence( - StructureMappingcommandSet[] colourBySequenceCommands) + public List executeCommand(final StructureCommandI command, + boolean getResponse) { - for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands) + if (chimeraManager == null || command == null) { - for (String command : cpdbbyseq.commands) - { - sendAsynchronousCommand(command, COLOURING_CHIMERA); + // ? thread running after viewer shut down + return null; + } + List reply = null; + // trim command or it may never find a match in the replyLog!! + String cmd = command.getCommand().trim(); + List lastReply = chimeraManager + .sendChimeraCommand(cmd, getResponse); + if (getResponse) + { + reply = lastReply; + if (Console.isDebugEnabled()) { + Console.debug( + "Response from command ('" + cmd + "') was:\n" + lastReply); } } - } - - /** - * @param files - * @param sr - * @param fr - * @param alignment - * @return - */ - @Override - protected StructureMappingcommandSet[] getColourBySequenceCommands( - String[] files, SequenceRenderer sr, FeatureRenderer fr, - AlignmentI alignment) - { - return ChimeraCommands.getColourBySequenceCommand(getSsm(), files, - getSequence(), sr, fr, alignment); - } - - /** - * @param command - */ - protected void executeWhenReady(String command) - { - waitForChimera(); - sendChimeraCommand(command, false); - waitForChimera(); - } - - private void waitForChimera() - { - while (viewer != null && viewer.isBusy()) + else { - try - { - Thread.sleep(15); - } catch (InterruptedException q) + if (Console.isDebugEnabled()) { + Console.debug("Command executed: " + cmd); } } - } - - // End StructureListener - // ////////////////////////// - /** - * instruct the Jalview binding to update the pdbentries vector if necessary - * prior to matching the viewer's contents to the list of structure files - * Jalview knows about. - */ - public abstract void refreshPdbEntries(); - - /** - * map between index of model filename returned from getPdbFile and the first - * index of models from this file in the viewer. Note - this is not trimmed - - * use getPdbFile to get number of unique models. - */ - private int _modelFileNameMap[]; + return reply; + } - // //////////////////////////////// - // /StructureListener @Override - public synchronized String[] getPdbFile() + public synchronized String[] getStructureFiles() { - if (viewer == null) + if (chimeraManager == null) { return new String[0]; } - return chimeraMaps.keySet().toArray( - modelFileNames = new String[chimeraMaps.size()]); + return chimeraMaps.keySet() + .toArray(modelFileNames = new String[chimeraMaps.size()]); } /** - * Construct and send a command to highlight zero, one or more atoms. We do - * this by sending an "rlabel" command to show the residue label at that - * position. + * Construct and send a command to highlight zero, one or more atoms. We do this + * by sending an "rlabel" command to show the residue label at that position. */ @Override public void highlightAtoms(List atoms) @@ -769,6 +377,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel return; } + boolean forChimeraX = chimeraManager.isChimeraX(); StringBuilder cmd = new StringBuilder(128); boolean first = true; boolean found = false; @@ -783,18 +392,26 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel { if (first) { - cmd.append("rlabel #").append(cms.get(0).getModelNumber()) - .append(":"); + cmd.append(forChimeraX ? "label #" : "rlabel #"); } else { cmd.append(","); } first = false; - cmd.append(pdbResNum); - if (!chain.equals(" ")) + if (forChimeraX) { - cmd.append(".").append(chain); + cmd.append(cms.get(0).getModelNumber()) + .append("/").append(chain).append(":").append(pdbResNum); + } + else + { + cmd.append(cms.get(0).getModelNumber()) + .append(":").append(pdbResNum); + if (!chain.equals(" ") && !forChimeraX) + { + cmd.append(".").append(chain); + } } found = true; } @@ -808,19 +425,29 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel { return; } - + if (!found) + { + // not a valid residue label command, so clear + cmd.setLength(0); + } /* - * unshow the label for the previous residue + * prepend with command + * to unshow the label for the previous residue */ if (lastHighlightCommand != null) { - viewer.sendChimeraCommand("~" + lastHighlightCommand, false); + cmd.insert(0, ";"); + cmd.insert(0,lastHighlightCommand); + cmd.insert(0,"~"); + } - if (found) - { - viewer.sendChimeraCommand(command, false); + if (cmd.length()>0) { + executeCommand(true, null, new StructureCommand(cmd.toString())); + } + + if (found) { + this.lastHighlightCommand = command; } - this.lastHighlightCommand = command; } /** @@ -831,65 +458,103 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel /* * Ask Chimera for its current selection */ - List selection = viewer.getSelectedResidueSpecs(); - - /* - * Parse model number, residue and chain for each selected position, - * formatted as #0:123.A or #1.2:87.B (#model.submodel:residue.chain) - */ - List atomSpecs = new ArrayList(); - for (String atomSpec : selection) + StructureCommandI command = getCommandGenerator().getSelectedResidues(); + + Runnable action = new Runnable() { - int colonPos = atomSpec.indexOf(":"); - if (colonPos == -1) + @Override + public void run() { - continue; // malformed + List chimeraReply = executeCommand(command, true); + + List selectedResidues = new ArrayList<>(); + if (chimeraReply != null) + { + /* + * expect 0, 1 or more lines of the format either + * Chimera: + * residue id #0:43.A type GLY + * ChimeraX: + * residue id /A:89 name THR index 88 + * We are only interested in the atomspec (third token of the reply) + */ + for (String inputLine : chimeraReply) + { + String[] inputLineParts = inputLine.split("\\s+"); + if (inputLineParts.length >= 5) + { + selectedResidues.add(inputLineParts[2]); + } + } + } + + /* + * Parse model number, residue and chain for each selected position, + * formatted as #0:123.A or #1.2:87.B (#model.submodel:residue.chain) + */ + List atomSpecs = convertStructureResiduesToAlignment( + selectedResidues); + + /* + * Broadcast the selection (which may be empty, if the user just cleared all + * selections) + */ + getSsm().mouseOverStructure(atomSpecs); + } + }; + new Thread(action).start(); + } - int hashPos = atomSpec.indexOf("#"); - String modelSubmodel = atomSpec.substring(hashPos + 1, colonPos); - int dotPos = modelSubmodel.indexOf("."); - int modelId = 0; + /** + * Converts a list of Chimera(X) atomspecs to a list of AtomSpec representing the + * corresponding residues (if any) in Jalview + * + * @param structureSelection + * @return + */ + protected List convertStructureResiduesToAlignment( + List structureSelection) + { + List atomSpecs = new ArrayList<>(); + for (String atomSpec : structureSelection) + { try { - modelId = Integer.valueOf(dotPos == -1 ? modelSubmodel - : modelSubmodel.substring(0, dotPos)); - } catch (NumberFormatException e) + AtomSpec spec = parseAtomSpec(atomSpec); + String pdbfilename = getPdbFileForModel(spec.getModelNumber()); + spec.setPdbFile(pdbfilename); + atomSpecs.add(spec); + } catch (IllegalArgumentException e) { - // ignore, default to model 0 + Console.error("Failed to parse atomspec: " + atomSpec); } + } + return atomSpecs; + } - String residueChain = atomSpec.substring(colonPos + 1); - dotPos = residueChain.indexOf("."); - int pdbResNum = Integer.parseInt(dotPos == -1 ? residueChain - : residueChain.substring(0, dotPos)); - - String chainId = dotPos == -1 ? "" : residueChain - .substring(dotPos + 1); - - /* - * Work out the pdbfilename from the model number - */ - String pdbfilename = modelFileNames[frameNo]; - findfileloop: for (String pdbfile : this.chimeraMaps.keySet()) + /** + * @param modelId + * @return + */ + protected String getPdbFileForModel(int modelId) + { + /* + * Work out the pdbfilename from the model number + */ + String pdbfilename = modelFileNames[0]; + findfileloop: for (String pdbfile : this.chimeraMaps.keySet()) + { + for (ChimeraModel cm : chimeraMaps.get(pdbfile)) { - for (ChimeraModel cm : chimeraMaps.get(pdbfile)) + if (cm.getModelNumber() == modelId) { - if (cm.getModelNumber() == modelId) - { - pdbfilename = pdbfile; - break findfileloop; - } + pdbfilename = pdbfile; + break findfileloop; } } - atomSpecs.add(new AtomSpec(pdbfilename, chainId, pdbResNum, 0)); } - - /* - * Broadcast the selection (which may be empty, if the user just cleared all - * selections) - */ - getSsm().mouseOverStructure(atomSpecs); + return pdbfilename; } private void log(String message) @@ -897,204 +562,241 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel System.err.println("## Chimera log: " + message); } - private void viewerCommandHistory(boolean enable) - { - // log("(Not yet implemented) History " - // + ((debug || enable) ? "on" : "off")); - } - - public long getLoadNotifiesHandled() - { - return loadNotifiesHandled; - } - - @Override - public void setJalviewColourScheme(ColourSchemeI cs) + /** + * Constructs and send commands to Chimera to set attributes on residues for + * features visible in Jalview. + *

+ * The syntax is: setattr r <attName> <attValue> <atomSpec> + *

+ * For example: setattr r jv_chain "Ferredoxin-1, Chloroplastic" #0:94.A + * + * @param avp + * @return + */ + public int sendFeaturesToViewer(AlignmentViewPanel avp) { - colourBySequence = false; + // TODO refactor as required to pull up to an interface - if (cs == null) + Map> featureValues = buildFeaturesMap( + avp); + List commands = getCommandGenerator() + .setAttributes(featureValues); + if (commands.size() > 10) { - return; + sendCommandsByFile(commands); } - - // Chimera expects RBG values in the range 0-1 - final double normalise = 255D; - viewerCommandHistory(false); - StringBuilder command = new StringBuilder(128); - - List residueSet = ResidueProperties.getResidues(isNucleotide(), - false); - for (String resName : residueSet) + else { - char res = resName.length() == 3 ? ResidueProperties - .getSingleCharacterCode(resName) : resName.charAt(0); - Color col = cs.findColour(res); - command.append("color " + col.getRed() / normalise + "," - + col.getGreen() / normalise + "," + col.getBlue() - / normalise + " ::" + resName + ";"); + executeCommands(commands, false, null); } - - sendAsynchronousCommand(command.toString(), COLOURING_CHIMERA); - viewerCommandHistory(true); - } - - /** - * called when the binding thinks the UI needs to be refreshed after a Chimera - * state change. this could be because structures were loaded, or because an - * error has occurred. - */ - public abstract void refreshGUI(); - - @Override - public void setLoadingFromArchive(boolean loadingFromArchive) - { - this.loadingFromArchive = loadingFromArchive; + return commands.size(); } /** + * Write commands to a temporary file, and send a command to Chimera to open the + * file as a commands script. For use when sending a large number of separate + * commands would overload the REST interface mechanism. * - * @return true if Chimeral is still restoring state or loading is still going - * on (see setFinsihedLoadingFromArchive) + * @param commands */ - @Override - public boolean isLoadingFromArchive() + protected void sendCommandsByFile(List commands) { - return loadingFromArchive && !loadingFinished; + try + { + File tmp = File.createTempFile("chim", getCommandFileExtension()); + tmp.deleteOnExit(); + PrintWriter out = new PrintWriter(new FileOutputStream(tmp)); + for (StructureCommandI command : commands) + { + out.println(command.getCommand()); + } + out.flush(); + out.close(); + String path = tmp.getAbsolutePath(); + StructureCommandI command = getCommandGenerator() + .openCommandFile(path); + executeCommand(false, null, command); + } catch (IOException e) + { + System.err.println("Sending commands to Chimera via file failed with " + + e.getMessage()); + } } /** - * modify flag which controls if sequence colouring events are honoured by the - * binding. Should be true for normal operation - * - * @param finishedLoading + * Returns the file extension required for a file of commands to be read by + * the structure viewer + * @return */ - @Override - public void setFinishedLoadingFromArchive(boolean finishedLoading) + protected String getCommandFileExtension() { - loadingFinished = finishedLoading; + return ".com"; } /** - * Send the Chimera 'background solid " command. + * Create features in Jalview for the given attribute name and structure + * residues. * - * @see https - * ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/background - * .html - * @param col - */ - @Override - public void setBackgroundColour(Color col) - { - viewerCommandHistory(false); - double normalise = 255D; - final String command = "background solid " + col.getRed() / normalise - + "," + col.getGreen() / normalise + "," + col.getBlue() - / normalise + ";"; - viewer.sendChimeraCommand(command, false); - viewerCommandHistory(true); - } - - /** - * Ask Chimera to save its session to the given file. Returns true if - * successful, else false. + * 

+   * The residue list should be 0, 1 or more reply lines of the format: 
+   *     residue id #0:5.A isHelix -155.000836316 index 5 
+   * or 
+   *     residue id #0:6.A isHelix None
+   *
* - * @param filepath - * @return + * @param attName + * @param residues + * @return the number of features added */ - public boolean saveSession(String filepath) + protected int createFeaturesForAttributes(String attName, + List residues) { - if (isChimeraRunning()) + int featuresAdded = 0; + String featureGroup = getViewerFeatureGroup(); + + for (String residue : residues) { - List reply = viewer.sendChimeraCommand("save " + filepath, - true); - if (reply.contains("Session written")) + AtomSpec spec = null; + String[] tokens = residue.split(" "); + if (tokens.length < 5) + { + continue; + } + String atomSpec = tokens[2]; + String attValue = tokens[4]; + + /* + * ignore 'None' (e.g. for phi) or 'False' (e.g. for isHelix) + */ + if ("None".equalsIgnoreCase(attValue) + || "False".equalsIgnoreCase(attValue)) + { + continue; + } + + try + { + spec = parseAtomSpec(atomSpec); + } catch (IllegalArgumentException e) + { + Console.error("Problem parsing atomspec " + atomSpec); + continue; + } + + String chainId = spec.getChain(); + String description = attValue; + float score = Float.NaN; + try { - return true; + score = Float.valueOf(attValue); + description = chainId; + } catch (NumberFormatException e) + { + // was not a float value } - else + + String pdbFile = getPdbFileForModel(spec.getModelNumber()); + spec.setPdbFile(pdbFile); + + List atoms = Collections.singletonList(spec); + + /* + * locate the mapped position in the alignment (if any) + */ + SearchResultsI sr = getSsm() + .findAlignmentPositionsForStructurePositions(atoms); + + /* + * expect one matched alignment position, or none + * (if the structure position is not mapped) + */ + for (SearchResultMatchI m : sr.getResults()) { - Cache.log - .error("Error saving Chimera session: " + reply.toString()); + SequenceI seq = m.getSequence(); + int start = m.getStart(); + int end = m.getEnd(); + SequenceFeature sf = new SequenceFeature(attName, description, + start, end, score, featureGroup); + // todo: should SequenceFeature have an explicit property for chain? + // note: repeating the action shouldn't duplicate features + if (seq.addSequenceFeature(sf)) + { + featuresAdded++; + } } } - return false; + return featuresAdded; } /** - * Ask Chimera to open a session file. Returns true if successful, else false. - * The filename must have a .py extension for this command to work. + * Answers the feature group name to apply to features created in Jalview from + * Chimera attributes * - * @param filepath * @return */ - public boolean openSession(String filepath) + protected String getViewerFeatureGroup() { - sendChimeraCommand("open " + filepath, true); - // todo: test for failure - how? - return true; + // todo pull up to interface + return CHIMERA_FEATURE_GROUP; } - /** - * Send a 'focus' command to Chimera to recentre the visible display - */ - public void focusView() + @Override + public String getModelIdForFile(String pdbFile) { - sendChimeraCommand("focus", false); + List foundModels = chimeraMaps.get(pdbFile); + if (foundModels != null && !foundModels.isEmpty()) + { + return String.valueOf(foundModels.get(0).getModelNumber()); + } + return ""; } /** - * Send a 'show' command for all atoms in the currently selected columns - * - * TODO: pull up to abstract structure viewer interface + * Answers a (possibly empty) list of attribute names in Chimera[X], excluding + * any which were added from Jalview * - * @param vp + * @return */ - public void highlightSelection(AlignmentViewPanel vp) + public List getChimeraAttributes() { - List cols = vp.getAlignViewport().getColumnSelection() - .getSelected(); - AlignmentI alignment = vp.getAlignment(); - StructureSelectionManager sm = getSsm(); - for (SequenceI seq : alignment.getSequences()) + List attributes = new ArrayList<>(); + StructureCommandI command = getCommandGenerator().listResidueAttributes(); + final List reply = executeCommand(command, true); + if (reply != null) { - /* - * convert selected columns into sequence positions - */ - int[] positions = new int[cols.size()]; - int i = 0; - for (Integer col : cols) + for (String inputLine : reply) { - positions[i++] = seq.findPosition(col); + String[] lineParts = inputLine.split("\\s"); + if (lineParts.length == 2 && lineParts[0].equals("resattr")) + { + String attName = lineParts[1]; + /* + * exclude attributes added from Jalview + */ + if (!attName.startsWith(ChimeraCommands.NAMESPACE_PREFIX)) + { + attributes.add(attName); + } + } } - sm.highlightStructure(this, seq, positions); } + return attributes; } - + /** + * Returns the file extension to use for a saved viewer session file (.py) + * + * @return + */ @Override - public List getChainNames() - { - return chainNames; - } - - public Hashtable getChainFile() - { - return chainFile; - } - - public List getChimeraModelByChain(String chain) + public String getSessionFileExtension() { - return chimeraMaps.get(chainFile.get(chain)); + return CHIMERA_SESSION_EXTENSION; } - public int getModelNoForChain(String chain) + @Override + public String getHelpURL() { - List foundModels = getChimeraModelByChain(chain); - if (foundModels != null && !foundModels.isEmpty()) - { - return foundModels.get(0).getModelNumber(); - } - return -1; + return "https://www.cgl.ucsf.edu/chimera/docs/UsersGuide"; } }